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Sample GSM2977029 Query DataSets for GSM2977029
Status Public on Mar 14, 2018
Title Sample_scr_cyto_m6A_rep2
Sample type SRA
 
Source name scr_cyto_m6A
Organism Mus musculus
Characteristics genotype/variation: scr
developmental stage: E14
cell type: murine embryonic stem cell
antibody: Rabbit anti-m6A (Synaptic, 202003)
molecule subtype: cytoplasmic RNA
Treatment protocol m6A-seq: RNA was fragmented and subject to immunoprecipitation with a m6A specific antibody. 
RNA-seq: RNAs were isolated from Zc3h13 knockdown, scramble knockdown and Zc3h13 rescue mouse ESCs. Polyadenylated RNA was extracted for library generation and sequencing.
RIP-seq: RNA was fragmented and subject to immunoprecipitation with a anti-Zc3h13 specific antibody. 
Growth protocol E14 murine embryonic stem cell was cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 1% none essential amino acid, 0.1% beta-mercaptoethanol, 100u/ml penicillin/ Streptomycin and 1000u LIF.
Extracted molecule total RNA
Extraction protocol Total RNAs from mESCs were isolated using Trizol reagent according to the manufacturer’s instruction (Life technology, 15596018). Polyadenylated RNAs were extracted by oligodT beads (NEB, S1419S), followed by removal of contaminated rRNA with RiboMinus transcriptome isolation kit (Life technologies, A15026).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model HiSeq X Ten
 
Data processing library strategy: m6A-seq
Basecalls performed using CASAVA version 1.4
m6A-seq:
m6A-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf --max-multihits 1 --prefilter-multihits -o m6A_thout mm9_assemblies m6A.fq
m6A peaks were called by exomePeak 2.13 package of of Bioconductor under default parameters.
Mapped m6A reads were transfer to bedgraph files for visualization using bedtools.
RNA-seq:
RNA-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Transcriptome is assemblied using cufflinks;differential expressed genes were identified by cuffdiff.
FPKM value of Ensembl genes were calculated by cufflinks.
RIP-seq:
RIP-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Zc3h13 protein RIP signal was calculated as FPKM by FPKM_count.
FPKM value of Ensembl genes were calculated by FPKM_count.
Genome_build: mm9
Supplementary_files_format_and_content:
bed files include m6A peak lists identified by exomePeaks; bedGraph files include the averaged m6A enriched density.
tab-delimited text file include the FPKM values of Refseq genes in Mus musculus genome;
tab-delimited text file include the genes with Zc3h13 binding on mRNA transcripts.
 
Submission date Feb 02, 2018
Last update date Mar 14, 2018
Contact name Ruitu Lyu
E-mail(s) lvruitu@gmail.com
Organization name Institutes of Biomedical Sciences Fudan University
Lab Epigenetics lab
Street address 138 Yixueyuan Road Xuhui District
City Shanghai
ZIP/Postal code 200030
Country China
 
Platform ID GPL21273
Series (1)
GSE94148 A novel RNA m6A modulator Zc3h13 plays an anchor role in facilitating nuclear RNA methylation and mouse embryonic stem cell self-renewal
Relations
BioSample SAMN08456688
SRA SRX3642951

Supplementary file Size Download File type/resource
GSM2977029_Sample_scr_m6A_cyto.rep2.bedGraph.gz 49.8 Mb (ftp)(http) BEDGRAPH
GSM2977029_Sample_scr_m6A_cyto_peaks.rep2.bed.gz 272.9 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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